Gaia CNV error TCGA data

Question

[s.lueong]

Dear All,

I am trying to analyze some TCGA CNV data using the GAIA package. I followed the tutorial from @kevinblighe. Everything runs well and at the end, the error below come up. Has someone witnessed this before anc could some one propose a solution.

I previously ran this code about a year ago and it worked well.

Thank you

> results.TCGT <- runGAIA(cnv_obj, markers_obj, "COAD_early.txt", chromosomes=1)

Performing Data Preprocessing

Done

Computing Discontinuity Matrix
.
Done
Computing Probability Distribution
....
Done
Assessing the Significance of Observed Data
..
Done
Writing COAD_early.txt.igv.gistic File for Integrative Genomics Viewer (IGV) Tool
..
Done
Running Homogeneous peel-off Algorithm With Significance Threshold of 0.25 and Homogenous Threshold of 0.12
.Error in if (tmp_list[[1]] == -1) { : the condition has length > 1

[Ram]

1. Don't use people's names as tags.
2. Format your post properly. I've done what I can for now.
3. Add a link to "the tutorial from Kevin Blighe ". He's written a whole bunch of them and you should link to the exact tutorial you're referring to.